I have read up on x-ray crystallography but can't see why it would be different for the transmembrabe portion. I think it could be to do with the size or complexity but to be honest i didnt quite understand how cyrstallography works anyway.

The crystallization of membrane proteins in toto is one of the “holy grails” of crystallography. There is no general way to do it and of the few cases that have succeeded, two (rhodopsin and F1-ATPase) won Nobel Prizes. Transmembrane regions of membrane and integral membrane proteins tend to be very hydrophobic. When you isolate such proteins devoid of lipd membranes, they very often form aggregates as the hydrophobic regions try to escape aqueous environments by clustering together—kind of like circling the wagons to exclude solvent. Aggregation of this sort is not usually compatible with crystallization because the protein-protein interactions are not very specific and, although crystallization is sort of an organized precipitation, you need to have specific, repeatable interactions to make a well-ordered, diffracting crystal. So why not crystallize the protein as it stands in a lipid bilayer, you may ask? It’s hard (nigh on impossible) to get 3D crystals out of lipid bilayers. If you get anything at all, you tend to get two-dimensional, planar assemblies of proteins within the bilayer. You can extract structural information from these kinds of assemblies, but usually it is low resolution information derived from diffraction experiments in an electron microscope, not from higher resolution x-rays; the resolution of 2D crystal structures used to be around 20-30 Å, but it has improved over the years and you can now get maybe 10 Å in favorable cases. Membrane protein crystallization remains one of the more challenging areas of protein crystallization, made all the more tantalizing to pharmaceutical companies who dearly wish to develop drugs that target membrane receptors and the like.